1) Shiina, T. (1988) Studies on characteristics of excitability of Nitellopsis plasmalemma. （東京大学理学博士1963号）
2) 岡与志男、片桐晃、椎名隆、杉山雅人、橋本史朗、花田禎一、馬場正昭、藤田英夫、堀智孝、堀部正吉、松原孝治、村中重利、山内淳、山本直一(1997)　無機定性分析実験　共立出版
3) 豊島喜則、椎名隆（2001）オルガネラの転写因子．「植物ゲノム機能のダイナミズム－転写因子による発現の制御－」シュプリンガー・フェアラーク社pp.219-237
4) 豊島喜則、椎名隆（2002）パーティクルガンによる外来遺伝子の導入と一過性発現　「細胞工学実験書　改訂版」日本生物工学会編　培風館　pp.231-236
5) 椎名隆 (2005) 葉緑体の形、食虫植物のメカニズム　「形の科学事典」朝倉書店　208-212
6) 山下博史，椎名隆 (2006)　接触傾性運動　ﾑ　食虫植物の捕虫メカニズムー　プラントミメティックス NTS出版
7) 椎名　隆　佐藤　雅彦　角山　雄一 (2007) スタートアップ生化学 化学同人
8) 椎名隆、石崎陽子 編訳（2011)　遺伝子組換え食品と有機農業　丸善
9) 椎名隆，八木祐介 (2014)　光合成遺伝子の光応答制御メカニズム　「光合成研究と産業応用最前線」NTS pp177-189
10) 椎名隆、石崎陽子（2015）“遺伝子組換え農業の可能性と課題“ 農業は、面白い!　 栗田治編　第５巻 pp1-114 アを中心とした植物の新しいカルシウム制御ネットワーク」

1) Shiina, T. and Tazawa, M. (1986) Action potential in Luffa cylindlica and its effects on elongation growth. Plant Cell Physiol. 27, 1081-1089
2) Shiina, T. And Tazawa, M. (1986) Regulation of membrane excitation by protein phosphorylation in Nitellopsis obtusa. Protoplasma 134, 60-61
3) Shiina, T. and Tazawa, M. (1987) Demonstration and chracterization of Ca2+ channel in tonoplast-free cells of Nitellopsis obtusa. J. Membrane Biol. 96, 263-276
4) Shiina, T. and Tazawa, M (1987) Ca2+-activated Cl- channel in plasmalemmma of Nitellopsis obtusa. J. Membrane Biol. 99, 137-146
5) Shiina, T., Wayne, R., Lim Tung, H.Y., and Tazawa, M. (1988) Possible involvement of protein phosphorylation/dephosphorylation in the modulation of Ca2+ channel in tonoplast-free cells of Nitellopsis.　J. Membrane Biol. 102, 255-264
6) Shiina, T. and Tazawa, M. (1988)　Ca2+-dependent Cl- efflux in tonoplast-free cells of Nitellopsis obtusa.　J. Membrane Biol. 106, 135-139
7) Miyazaki, A., Shiina, T., Toyoshima, Y., Gounaris, K. and Barber, J. (1989)　Stoichiometry of cytochrome b-559 in photosystem II.　Biochim Biophys.Acta 975, 142-147
8) Kawaguchi, H., Fukuda, I., Shiina, T. and Toyoshima, Y. (1992)　Dynamical behavior of psb gene transcripts in greening wheat seedlings. I. Time course of accumulation of the psbA through psbN gene transcripts during light-induced greening. 　Plant. Mol. Biol., 20: 695-704
9) Araga, C., Akabori, K., Sasaki, J., Maeda, A., Shiina, T. and Toyoshima, Y.(1993) Functional reconstitution of the primary quinone acceptor, QA, in the photosystem II core complexes. Biochim. Biophys. Acta, 1142: 36-42
10) Kitamura, K., Ozawa, S., Shiina, T. and Toyoshima, Y. (1994) L protein, encoded by psbL, recovers normal functioning of the primary quinone acceptor, QA, in the isolated D1/D2/CP47/Cytb-559/I photosystem II reaction center core complex. FEBS Lett. 354: 113-116
11) Wada, T., Tunoyama, Y., Shiina, T. and Toyoshima, Y. (1994) In vitro analysis of light-induced transcription in the wheat psbD/C gene cluster using plastid extracts from dark-grown and short-term-illuminated seedlings. Plant Physiol. 104: 1259-1267
12) Ozawa, S., Kobayashi, T., Sugiyama, R., Hoshida, H., Shiina , T. and Toyoshima, Y. (1997) Role of PSII-L protein (psbL gene product) on the electron transfer in photosystem II complex. I. Over production of wild-type and mutant versions of PSII-L protein and reconstitution into the PSII core complex. Plant Mol. Biol. 34: 151-161
13) Satoh, J., Baba, K., Nakahira, Y., Shiina, T. and Toyoshima, Y. (1997) Characterization of dynamics of the psbD light-induced transcription in mature wheat chloroplasts. Plant Mol. Biol. 33: 267-278
14) Hoshida, H., Sugiyama, R., Nakano, Y., Shiina, T. and Toyoshima, Y. (1997) Electron paramagnetic resonance and mutational analyses revealed the involvement of Photosystem II-L subunit in the oxidation step of Tyr-Z by P680+ to form the Tyr-Z+P680Pheo- state in photosystem II. Biochemistry 36 :12053-12061
15) Shiina, T., Nishii, A., Toyoshima, Y. and Bogorad, L. (1997) Identification of promoter elements involved in the cytosolic Ca2+-mediated photoregulation of maize cab-m1 expression. Plant Physiol. 115: 477-483
16) Nakahira, Y., Baba, K., Yoneda, A., Shiina, T. and Toyoshima, Y. (1998) Circadian-regulated transcription of the psbD light-responsive promoter in wheat chloroplasts. Plant Physiol. 118, 1079-1088
17) Shiina, T., Allison, L. and Maliga, P. (1998) rbcL transcript levels in tobacco plastids are independent of light: reduced dark transcription rate is compensated by increased mRNA stability. Plant Cell 10, 1713-1722
18) Satoh, J., Baba, K., Nakahira,, Y., Tsunoyama, Y., Shiina, T. and Toyoshima, Y (1999) Developmental stage-specific multi-subunit plastid RNA polymerases (PEP) in wheat. Plant J 18, 407-416
19) Morikawa, K, Itoh, S., Tsunoyama, Y., Nakahira, Y., Shiina, T. and Toyoshima, Y. (1999) Circadian-regulated expression of a nuclear-encoded plastid ??factor gene (sigA ) in wheat seedlings. FEBS Lett.451, 275-278
20) Ogihara, Y., Isono, K., Kojima, T., Endo, A., Hanaoka, M., Shiina, T., Terachi, T., Utsugi, S., Murata, M., Mori, N., Takumi, S., Ikeo, K., Gojobori, T., Murai, R., Murai, K., Matsuoka, Y., Ohnishi, Y., Tajiri, H. and Tsunewaki, K. (2000) Chinese Spring wheat (Triticum aestivum L.) chloroplast genome: complete sequence and contig clones. Plant Molecular Biology Reporter 18, 243-253
21) Shiina, T., Hayashi, K., Ishii, N., Morikawa K. and Toyoshima, Y. (2000) Chloroplast tubules visualized in transplastomic plants expressing green fluorescent protein. Plant Cell Physiol. 41, 367-371
22) Ogihara, Y., Isono, K., Kojima, T., Endo, A., Hanaoka, M., Shiina, T., Terachi, T., Utsugi, S., Murata, M., Mori, N., Takumi, S., Ikeo, K., Gojobori, T., Murai, R., Murai, K., Matsuoka, Y., Ohnishi, Y., Tajiri, H. and Tsunewaki, K. (2002) Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Genet Genomics 266, 740-746
23) Morikawa,K., Shiina, T., Murakami, S., Toyoshima, Y. (2002) Novel nuclear-encoded proteins interacting with a plastid sigma factor, Sig1, in Arabidopsis thaliana. FEBS Lett. 514, 300-304
24) Tsunoyama, Y., Morikawa, K., Shiina, T. Toyoshima, Y. (2002) Blue light specific and differential expression of a plastid ? factor, Sig5 in Arabidopsis thaliana. FEBS Lett. 516, 225-228
25) Hayashi, K., Shiina, T., Ishii, N., Iwai, K., Ishizaki, Y., Morikawa, K., Toyoshima, Y. (2003) A role of the -35 element in the initiation of transcription at psbA promoter in tobacco plastids. Plant Cell Physiol.44 334-341 NEDO
26) Tsunoyama Y, Ishizaki Y, Morikawa K, Kobori M, Nakahira Y, Takeba G, Toyoshima Y, Shiina T. (2004) Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. PNAS, 101, 3304-3309 NEDO
27) Baba, K., Schmidt, J., Espinosa-Ruiz, A., Villarejo, A., Shiina, T., Gardestrom, P., Sane, A.P., Bhalerao, P. (2004) Organellar gene transcription and early seedling development are affected in the rpoT;2 mutant of Arabidopsis. Plant J. 38, 38-48 NEDO
28) Ishizaki, Y., Tsunoyama, Y., Hatano, K., Ando, K., Kato, K., Shinmyo, A., Kobori, M., Takeba, G., Nakahira, Y. Shiina, T. (2005) A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J. 42, 133-144 NEDO
29) Ogihara Y, Yamazaki Y, Murai K, Kanno A, Terachi T, Shiina T, Miyashita N, Nasuda S, Nakamura C, Mori N, Takumi S, Murata M, Futo S, Tsunewaki K. (2005) Structural dynamics of cereal mitochondrial genome as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucl. Acid Res. 33, 6235-6250
30) Shiina, T., Tsunoyama, Y., Nakahira, Y., Khan, M.S. (2005) Plastid RNA polymerases, promoters and transcription regulators in higher plants. Int. Rev. Cytology 244, 1-68 NEDO
31) Toyoshima, Y., Onda, Y., Shiina, T., Nakahira, Y. (2005) Plastid transcription in higher plants. Crit. Rev. Plant Sci. 24, 59-81 NEDO
32) Khan MS, Hameed W, Nozoe M, Shiina T (2007) Disruption of the psbA gene by the copy correction mechanism reveals that the expression of plastid-encoded genes is regulated by photosynthesis activity. J Plant Res. 120, 421-430 NEDO
33) Bang WY, Jeong IS, Kim DW, Im CH, Ji C, Hwang SM, Kim SW, Son YS, Jeong J, Shiina T, Bahk JD. (2008) Role of Arabidopsis CHL27 protein for photosynthesis, chloroplast development and gene expression profiling. Plant Cell Physiol. 49, 350-63.
34) Hashimoto K, Igarashi H, Mano S, Takenaka C, Shiina T, Yamaguchi M, Demura T, Nishimura M, Shimmen T, Yokota E. (2008) An isoform of Arabidopsis myosin XI interacts with small GTPases in its C-terminal tail region. J Exp Bot. 59, 3523-31
35) Suwastika IN, Uemura T, Shiina T, Sato MH, Takeyasu K. (2008) SYP71, a Plant-specific Qc-SNARE Protein, Reveals Dual Localization to the Plasma Membrane and the Endoplasmic Reticulum in Arabidopsis. Cell Struct Funct. 33: 185 - 192
36) Nomura H, Komori T, Kobori M, Nakahira Y, Shiina T. (2008) Evidence for chloroplast control of external Ca2+-induced cytosolic Ca2+ transients and stomatal closure. Plant J. 53, 988-98 NEDO
37) Shiina, T., Ishizaki, Y., Yagi, Y. Nakahira, Y.(2009) Function and evolution of plastid sigma factors. Plant Biotechnology 26, 57-66 NEDO
38) Bang WY, Hata A, Jeong IS, Umeda T, Masuda T, Chen J, Yoko I, Suwastika IN, Kim DW, Im CH, Lee BH, Lee Y, Lee KW, Shiina T, Bahk JD. (2009) AtObgC, a plant ortholog of bacterial Obg, is a chloroplast-targeting GTPase essential for early embryogenesis. Plant Mol Biol. 71, 379-90
39) Hasegawa M, Shiina T, Terazima M, Kumazaki S. (2010) Selective excitation of photosystems in chloroplasts inside plant leaves observed by near-infrared laser-based fluorescence spectral microscopy. Plant Cell Physiol. 51, 225-38.
40) Sugimoto T, Bamba T, Izumi Y, Nomura H, Shiina T, Fukusaki E. (2011) Use of ultra-performance liquid chromatography/time-of-flight mass spectrometry with nozzle-skimmer fragmentation for comprehensive quantitative analysis of secondary metabolites in Arabidopsis thaliana. J Sep Sci. 34, 3587-96
41) Im CH, Hwang SM, Son YS, Heo JB, Bang WY, Suwastika IN, Shiina T, Bahk JD. (2011) Nuclear/nucleolar GTPase 2 proteins as a subfamily of YlqF/YawG GTPases function in pre-60S ribosomal subunit maturation of mono- and dicotyledonous plants. J Biol Chem. 286, 8620-32
42) Koeda S, Hosokawa M, Kang BC, Tanaka C, Choi D, Sano S, Shiina T, Doi M, Yazawa S. (2012) Defense response of a pepper cultivar cv. Sy-2 is induced at temperatures below 24°C. J Plant Res. 125, 137-45
43) Bang WY, Chen J, Jeong IS, Kim SW, Kim CW, Jung HS, Lee KH, Kweon HS, Yoko I, Shiina T, Bahk JD. (2012) Functional characterization of ObgC in ribosome biogenesis during chloroplast development. Plant J. 71, 122-34
44) Yagi Y, Ishizaki Y, Nakahira Y, Tozawa Y, Shiina T. (2012) Eukaryotic-type plastid nucleoid protein pTAC3 is essential for transcription by the bacterial-type plastid RNA polymerase. Proc Natl Acad Sci U S A. 109, 7541-6
45) Nomura H, Komori T, Uemura S, Kanda Y, Shimotani K, Nakai K, Furuichi T, Takebayashi K, Sugimoto T, Sano S, Suwastika IN, Fukusaki E, Yoshioka H, Nakahira Y, Shiina T. (2012) Chloroplast-mediated activation of plant immune signalling in Arabidopsis. Nat Commun. 26;3:926. doi: 10.1038/ncomms1926.
46) Yagi Y, Shiina T. (2012) Evolutionary aspects of plastid proteins involved in transcription: The transcription of a tiny genome is mediated by a complicated machinery. Transcription. 3, 1-5
47) Nakai Y, Nakahira Y, Sumida H, Takebayashi K, Nagasawa Y, Yamasaki K, Akiyama M, Ohme-Takagi M, Fujiwara S, Shiina T, Mitsuda N, Fukusaki E, Kubo Y, Sato MH. (2013) Vascular plant one-zinc-finger protein 1/2 transcription factors regulate abiotic and biotic stress responses in Arabidopsis. Plant J. 2013 73, 761-75
48) Yamasaki K, Motomura Y, Yagi Y, Nomura H, Kikuchi S, Nakai M, Shiina T. (2013) Chloroplast envelope localization of EDS5, an essential factor for salicylic acid biosynthesis in Arabidopsis thaliana. Plant Signal Behav. 8, e23603
49) Nakahira Y, Ishikawa K, Tanaka K, Tozawa Y, Shiina T. (2013) Overproduction of hyperthermostable β-1,4-endoglucanase from the archaeon Pyrococcus horikoshii by tobacco chloroplast engineering. Biosci Biotechnol Biochem. 77, 2140-3
50) Yagi, Y and Shiina, T. (2014) Recent advances in the study of chloroplast gene expression and its evolution. Front. in Plant Sci. 5, 61
51) Nomura, H. and Shiina, T. (2014) Calcium signaling in plant endosymbiotic organelles: mechanism and role in physiology. Mol. Plant 7, 1094-1104
52) Radka Slovak, Christian Goschl, Xiaoxue Su, Koji Shimotani, Takashi Shiina and Wolfgang Busch (2014) A scalable open-source pipeline for large-scale root phenotyping. Plant Cell 26, 2390-2403
53) Sano S, Aoyama M, Nakai K, Shimotani K, Yamasaki K, Sato MH, Tojo D, Suwastika IN, Nomura H, Shiina T. (2014) Light-dependent expression of flg22-induced defense genes in Arabidopsis. Front Plant Sci. 5, 531
54) Suwastika IN, Denawa M, Yomogihara S, Im CH, Bang WY, Ohniwa RL, Bahk JD, Takeyasu K, Shiina T. (2014) Evidence for lateral gene transfer (LGT) in the evolution of eubacteria-derived small GTPases in plant organelles. Front Plant Sci. 5, 678

55) 椎名隆、田沢仁（1987）植物細胞のCa2+チャンネル　生体の科学　38、 557-561
56) 椎名隆、和田拓治、角山雄一、豊島喜則（1992）葉緑体遺伝子の光による転写制御 ＲIニュース、12、2-3
57) 椎名隆（1994）核コードの因子による葉緑体にコードされた遺伝子の発現制御機構 Radioisotopes 43, 75-76
58) 中平洋一，椎名隆　(2005)　葉緑体の秘めたるパワー　蛋白質・核酸・酵素 50　50, 1918-1920